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Optimizing and Benchmarking De Novo Hara et al. BMC Genomics (2015) 16:977 DOI 10.1186/s12864-015-2007-1 RESEARCH ARTICLE Open Access Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation Yuichiro Hara1, Kaori Tatsumi1, Michio Yoshida2, Eriko Kajikawa2, Hiroshi Kiyonari3,4 and Shigehiro Kuraku1* Abstract Background: RNA-seq enables gene expression profiling in selected spatiotemporal windows and yields massive sequence information with relatively low cost and time investment, even for non-model species. However, there remains a large room for optimizing its workflow, in order to take full advantage of continuously developing sequencing capacity. Method: Transcriptome sequencing for three embryonic stages of Madagascar ground gecko (Paroedura picta)was performed with the Illumina platform. The output reads were assembled de novo for reconstructing transcript sequences. In order to evaluate the completeness of transcriptome assemblies, we prepared a reference gene set consisting of vertebrate one-to-one orthologs. Result: To take advantage of increased read length of >150 nt, we demonstrated shortened RNA fragmentation time, which resulted in a dramatic shift of insert size distribution. To evaluate products of multiple de novo assembly runs incorporating reads with different RNA sources, read lengths, and insert sizes, we introduce a new reference gene set, core vertebrate genes (CVG), consisting of 233 genes that are shared as one-to-one orthologs by all vertebrate genomes examined (29 species)., The completeness assessment performed by the computational pipelines CEGMA and BUSCO referring to CVG, demonstrated higher accuracy and resolution than with the gene set previously established for this purpose. As a result of the assessment with CVG, we have derived the most comprehensive transcript sequence set of the Madagascar ground gecko by means of assembling individual libraries followed by clustering the assembled sequences based on their overall similarities. Conclusion: Our results provide several insights into optimizing de novo RNA-seq workflow, including the coordination between library insert size and read length, which manifested in improved connectivity of assemblies. The approach and assembly assessment with CVG demonstrated here would be applicable to transcriptome analysis of other species as well as whole genome analyses. Keywords: RNA-seq, Transcriptome sequencing, de novo assembly, Completeness assessment, Library insert length, CVG (core vertebrate genes), Madagascar ground gecko Background compactness enables economical and rapid processing of Transcriptome sequencing (RNA-seq) has become a sequencing and data analysis, which could be further im- standard strategy to capture the spatiotemporal expression proved via the optimization of various of parameters of a genome. It has been applied to diverse organisms in- present in sample preparation, de novo short read assem- cluding those with limited prior sequence information, bly, and assembly product evaluation. usually denoted as ‘non-model’ species [1–3]. RNA-seq Modern high-throughput sequencers provide diverse targets transcribed regions that account for a minor frac- sequencing modes with variable read lengths, read types tion of whole genomes, at least in metazoans [4]. This (single read or paired-end read), and data sizes per run. Obviously, the choice of which sequencing mode to use influences the coverage of the transcriptome in de novo * Correspondence: [email protected] 1Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 sequencing projects targeting sequence discovery, as well Minatojima-minami, Chuo-ku, Kobe, Hyogo 650-0047, Japan as influencing expression profiling in differential gene Full list of author information is available at the end of the article © 2015 Hara et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Hara et al. BMC Genomics (2015) 16:977 Page 2 of 12 expression analyses. However, sample preparation proto- pombe, Caenorhabditis elegans, Drosophila melanogaster, cols for many existing commercial kits do not provide and Homo sapiens), and reports the coverage of protein- practical instructions about their suitability for individual coding genes in a particular set of assembled sequences purposes and sequencing modes. For RNA-seq library [16]. Intuitively, executing CEGMA referring to a rigor- preparation, there are few that introduce a choice of insert ously selected 248 gene subset of the 458 CEGs, which lengths with variable conditions for RNA fragmentation. is composed of conserved genes with no or minimal For example, the standard protocol for Illumina TruSeq paralog(s) from, is expected to yield accurate complete- RNA Sample Prep Kit recommends intensive RNA frag- ness assessment [17]. In reality, however, our preliminary mentation, which results in a high proportion of library analysis has shown that some CEGs have paralogs molecules with the middle of their inserts sequenced from potentially misidentified as orthologs. both ends. To maximize the potential of obtaining longer In this study, we reconstructed embryonic transcrip- reads, it is preferable to prepare libraries with longer tomes of the Madagascar ground gecko (Paroedura inserts using moderate RNA fragmentation. picta) (Fig. 1a). This species has a variety of benefits Several computational programs employing short for use in developmental biology, including the avail- reads have been developed for producing de novo tran- ability of an elaborate embryonic staging system, scriptome assemblies [5–8]. Typical challenges in de feasibility of in ovo operational experiments, and non- novo transcriptome assembly include large variation of seasonal high reproductivity [18–21]. In the reptilian expression levels among transcripts, sequencing bias, order Squamata, large-scale sequence information is and alternative splicing [6]. Merging multiple assemblies publicly available for anole lizard, Burmese python, based on different k-mer lengths is an effective way of and king cobra. Within Squamata, the lineage leading to improving transcriptome assemblies because each tran- Gekkonidae, to which the Madagascar ground gecko be- script has different degrees of abundances [5, 9]. Thus, longs, diverged from the lineage containing the above many of the transcriptome assemblers implement the mentioned species approximately 200 million years ago multiple k-mer approach. On the other hand, Trinity, one (Fig. 1b) [22]. The phylogenetic position emphasizes the of the most widely used transcriptome assemblers, allows importance of producing sequence information for this only a fixed k-mer value (k = 25) when it is employed as a animal lineage. full program package [6]. So far, both Trinity and the mul- tiple k-mer approaches have provided reasonable assembly results [10, 11]. De novo transcriptome assemblies are sometimes used as references to which short reads are ACB mapped when transcriptome profiles are compared be- tween multiple samples [12–14]. In such differential ex- pression analyses, the mapping target, usually called the ‘reference’ assembly, is made from short reads from mul- tiple sample sources, which requires a process that merges the sequences into one assembly. This merging can be D hindered by among-sample variation of expression levels gecko of individual genes and genetic backgrounds. To cope green anole* with these difficulties, it is worthwhile to analyze multiple Burmese python* methods for merging assemblies, provided that the king cobra* merged assemblies are compared and evaluated on rea- tuatara sonable grounds (see [11]). chicken* Evaluating de novo assembly products requires a Chinese alligator* multi-faceted assessment [15]. N50 length, a weighted Chinese softshell turtle* median of assembly sequence lengths, is a widely used mammals metric but does not give any clue about the complete- 300 200 100 0 ness of the contents of the assembly, such as protein- (MYA) coding genes. This aspect of assembly evaluation could Fig. 1 Animals used in this study. a Embryo of Madagascar ground be satisfied through the use of the pipeline CEGMA gecko at four days before estimated date of oviposition (−4 days (Core Eukaryotic Genes Mapping Approach) [16, 17]. post oviposition, −4 dpo). b 9 dpo embryo. c 30 dpo embryo. Scale CEGMA makes use of 458 core eukaryotic genes bars, 2 mm. d Molecular phylogenetic relationship between the (CEGs), with each gene consisting of orthologs that are gecko and other amniotes. Asterisks indicate the sauropsid species conserved among six eukaryotic species (Arabidopsis for which whole genome sequences have been published. Divergence times were based on the TimeTree project [22] thaliana, Saccharomyces cerevisiae, Schizosaccharomyces Hara et al. BMC Genomics (2015) 16:977 Page 3 of 12 For efficient data production, we introduced modifica- distribution compared to Library A (349 bp on aver- tions to a standard library preparation protocol to in- age; Fig. 2). Additionally,
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